I guess our main omega was in heat and that alfa just happened to be around this impregnated him, then our omega ran away sacred cause he was just raped. Alfa boi didnt think much of it cause to him its just a one night stand!
Given the thoughts Kairi has about Jinguu, the way he acts around him and his honest desire to see him happy with a marriage partner we can infer he wasn't raped...check out the spoiler... http://www.mangago.zone/home/mangatopic/3745560/
In the older chapter when he said "we arent kids anymore" i knew he had a weird childhood exprience that made him this it was normal between kids.